Intruder
by stella-pegasi
Summary: There is an intruder on Atlantis, who may cost John Sheppard his life.


**Title:** **Intruder**

**Author**: _stella_pegasi_

**Rating: **K +

**Genres: **Action, hurt/comfort

**Word Count: **~16,800

**Spoilers: **Approximately Mid-third Season

**Warnings:** Minor Language

**Characters:** John Sheppard, Rodney McKay, Ronon Dex, Teyla Emmagan, Carson Beckett, Elizabeth Weir, Evan Lorne

**Summary:** There is an intruder on Atlantis, who may cost John Sheppard his life.

**Disclaimer: **I do not own them; I would have treated them better.

**Author's Notes: **First, to all of you waiting for an update to Road Trip it is coming. I apologize for the delay, it was not intentional. Real life has been kicking my you know what and I promised myself I would finish my novel by December 1 and I did…now in edit and hoping to find an agent. So…my first love, SGA took a backseat for a while.

One of my dearest friends talked me into writing for the sheppard_hc Secret Santa 2012, so I wrote this before I turn back to Road Trip and a story I have promised to someone. So, expect a Road Trip update soon. And thank you to all of you who have contacted me and who have been enjoying the boys on the road I hope you will like Intruder. It was written as a give for ArtisticAbandon.

* * *

**Intruder**

by stella_pegasi

John Sheppard moved silently along the darkened passageway, trying to concentrate on the soothing resonance of the waves lapping at Atlantis' hull. Night after night, he roamed unexplored sections of the city, trying to escape the sounds in his head.

Without thinking, he changed direction abruptly and exited the passageway onto the deck; the doors opening without a conscious thought. He sucked in salty fresh air, rubbing his temples as he exhaled. Nothing helped; the sounds remained. In the bright moonlight, he walked to the railing surrounding the open section of the hull nicknamed the canal, and peered over the side, gazing at the inflatable rafts special ops used to train divers. The small rafts bobbed up and down with the gentle waves.

Leaning his elbows on the railing, he cradled his pounding head, making a vain attempt to will away the pain. But the sensation wouldn't go away; the nagging feeling that someone was calling his name, that someone was with him. An impression of urgency, yet when he tried to concentrate, he couldn't quite grasp the thought.

Sheppard was exhausted, sleep elusive, hindered by the pain. People were beginning to notice; Weir asked him at the morning briefing if he was all right, while Lorne caught him napping in the middle of the afternoon. At dinner, Teyla's telltale eyebrow arched when he told her he was fine; she clearly didn't believe him. After dinner, when he heard Beckett was looking for him, he knew she'd tattled. He never cared for busybodies; he was just fine.

He scoffed, "Yeah, John, keep telling yourself that; you're just fine."

He blew out a deep breath, knowing he wasn't fine and debating with himself about going to Beckett. He hadn't quite convinced himself when a claxon blared, the loud, grating sound startling him as intense pain flooded his head. Grabbing his head, he lost his footing and slipped over the railing, landing in one of the inflatable rafts, unconscious.

~ooOoo~

Dr. Elizabeth Weir stood, arms crossed, glaring at Senior Gate Technician Lt. Chuck Campbell. "What do you mean you can't find him? How can you possibly not know where Colonel Sheppard is?"

"Ma'am, he's not in his quarters, and his team hasn't seen him since dinner. Teyla and Ronon are tracing his normal running route to see if he decided to go for a run."

She sighed, "He couldn't…" the claxon blared again, interrupting her. Through gritted teeth, she said, "Can you turn that thing off?"

Chuck quickly pressed a series of crystals on the control panel, "Sorry, Dr. Weir, I thought I had turned it off."

"As I was saying, Sheppard didn't just vanish, get Lorne up here."

From behind her, Major Lorne answered, "I'm here, ma'am."

Whirling around, she said, "Have you started a search for the colonel?"

"Yes, ma'am; I have teams sweeping Atlantis."

"Have we done a sensor search for him?" Weir asked, glancing back at Chuck, who nodded.

"Yes, but nothing; can't raise his COM, either."

"Well, he didn't just vanish and with this alarm going off, it's out of character for him not to be here to see what's going on. Find him, major."

Lorne nodded, turned, and hurried down the gate room steps, passing a disheveled Dr. Rodney McKay on the way. McKay was engrossed in his pad display as he walked into the control room. Weir waited for a few moments, absently tapping her foot, until McKay decided to speak.

"I don't know why the alarm went off."

Weir leaned against a console, "You don't know why?" McKay shrugged and Weir continued, "Does anyone know anything around here?" McKay started to answer but she kept talking, "A very loud and quite annoying alarm, which we have never heard before and didn't know existed, goes off. and you have no idea why?"

"Elizabeth, we've been on Atlantis for over three years, but there's a lot we don't know about this place. So far, we are seeing some energy spikes in a section of the city that was flooded. It could be that some equipment has been activated and is shorting out; Zelenka has taken a team to investigate."

"Then why aren't you with them, Doctor?"

"Uh…you want me to go…with…" McKay nodded, "Going there now…" He started to leave but turned back, "No word about Sheppard?" Weir shook her head, and with a worried look on his face, McKay left, grabbing a Marine to accompany him.

~ooOoo~

Teyla and Ronon caught up with Major Lorne, as he was about to enter Sheppard's quarters.

Ronon grunted, "Checked out his favorite path, nothing."

Lorne punched in the override code and opened Sheppard's door, "Nothing yet from any of the search teams, either." They entered to find Sheppard's quarters in its normal pristine shape.

Teyla remarked, "The bed has not been slept in, and it is nearly 0400 now. Major, have you noticed anything out of sorts with the colonel lately?"

"Other than taking a nap in his office this afternoon, or that he looks exhausted? Yeah, I was beginning to worry."

"As were we, Major. I spoke to Doctor Beckett this evening regarding my concerns." Her eyes widened as she realized perhaps Sheppard could be in the infirmary; she asked, "You have checked the infirmary."

"This is Colonel Sheppard we're talking about; the infirmary was the first place I looked."

Ronon peered into the bathroom, "He's not here; we're wasting time."

The trio stepped into the hallway as the voice of one of the search team leaders erupted from their COMs. "Major, we found Colonel Sheppard's COM on the deck next to EP canal two."

At a dead run, Lorne tapped his COM, "On our way."

By the time, Lorne, Ronon, and Teyla arrived, the Marines had set up spotlights, and divers were about to enter the water. Ronon nearly jumped the railing before Lorne stopped him.

"No, let the rescue divers go in."

Ronon was about to argue when one of the Marines holding a handheld searchlight yelled, "I've got him; he's in one of the rafts."

The divers immediately vaulted over the side, as the others hung over the railing, holding their collective breath until the first diver reached the raft Sheppard was lying in. A thumbs-up from the diver elicited an audible sigh of relief from everyone; Sheppard was alive. Lorne ordered a litter and called for Beckett and a medical team.

Working quickly, the Marine SAR unit raised Sheppard from the raft, a diver riding along to keep the litter from striking the hull. Beckett and his team rushed toward the colonel as the diver unhooked from the harness.

"Doctor, he's unconscious, felt a huge lump on the right side of his skull. I think he might have hit his head on the motor."

"Thanks, lad." Beckett turned to the EMTs, "Lift this litter onto the gurney and let's get him to the infirmary."

Twenty minutes later, Elizabeth Weir and Rodney McKay rushed into the infirmary from opposite directions, nearly colliding. They found Ronon and Teyla waiting for Beckett to finish his preliminary exam on Sheppard. At Weir's silent question, Teyla answered, "We do not know anything at the moment, only that he is unconscious."

Turning to McKay, Weir asked, "Why didn't we find him with the sensors?"

"We've experienced scanning issues with that area. There's a major power conduit running along the water's edge at that particular canal, seems to block the scans. Sheppard told me that the SOs use that particular canal because it has ladder access to the waterline. Leave it to Sheppard to be in the one area where we couldn't find him."

"Did you find anything on the West Pier?"

"Nothing so far but there is something going on. We traced a power surge to a corridor on the seventh floor in the circular tower. But we can't access any of the rooms on the level; I sent Lorne to see if he can open it but his gene isn't as strong as Sheppard or Beckett's, so I doubt he can."

"You can't bypass it?"

"No, there are no door controls, believe me if there were, we'd be in there by now if …" McKay stopped as Beckett approached them, his expression worried.

"The good news is Colonel Sheppard's vitals signs are stable, somewhat weak but stable. The not so good news is he has a mild concussion with some slight swelling from the blow he took above his right ear, and along with some minor bleeding in the ear canal." Beckett paused, pursing his lips.

Quietly, Weir asked, "What else?"

"I…I don't know; the Ancient scanner revealed his brain activity is very elevated."

McKay asked, "Elevated, how?"

"The activity level is considerably stronger than in a healthy individual, much less someone with a head injury. Let me show you." Beckett walked over to a terminal and brought up a digital scan, "It's a mess; this is today's scan, compared to the colonel's baseline scan taken shortly after we arrived. You can see similarities here, and here," as he pointed, "but these other lines, I don't know why they are present."

Teyla asked, "Is he in any danger?"

Beckett shrugged, "I simply don't know how to answer that; once he regains consciousness we'll know more. Elizabeth, Teyla came to me after dinner to tell me that John has been acting very strangely the last couple of weeks. He complained of headaches, seemed to become increasingly tired as the days passed. Have you noticed anything?"

"Yes, I spoke to him this morning after the briefing. He looked exhausted, distracted; I was worried. Of course, he told me he was fine, but I didn't believe him."

"Fine…" Beckett murmured, "No... he is far from fine."

~ooOoo~

The familiar silhouette of Atlantis' gate room materialized, as awareness crept into Sheppard's consciousness. He felt disoriented, not certain how he ended up in the gate room; he was just on the South pier. Slowly, he pivoted in the darkened chamber to discover the stargate glowing, pale aqua light casting faint shadows on the walls.

As he climbed the steps toward the control room, the embedded lights engaged. Glancing around Sheppard realized he was alone and his heart thumped wildly in his chest. Where was everyone? As he pushed back against the adrenaline coursing through his body, he realized he wasn't alone, he sensed a presence. An elusive presence he couldn't identify.

Reaching the top landing, he walked to the stained-glass windows, revealing the city's shimmering outline. Atlantis was underwater, as it was when they arrived. He stood mesmerized by the view, confusion replacing anxiety. He felt much like he did as he passed through the gate that day, a sense that somehow he was responsible for the city coming alive.

Whispering, he chastised himself, "The gene only activates equipment; it doesn't control the city…"

_"…Trust…."_

A wispy voice echoed in the quiet; startled Sheppard turned toward the gate. "Who's there?"

_"You know…"_

"No, I don't…" he stopped. He did know; he had known since the first thought entered his consciousness, "Atlantis."

As he uttered the city's name, awareness surged into his mind, bringing white-hot pain; the image of the gate faded into darkness.

~ooOoo~

The infirmary was dark, only the dim light above Sheppard's bed and the soft glow from the monitors revealed his team. Teyla sat quietly; her head bowed, meditating. Ronon slouched in a chair next to Sheppard's bed. Rodney McKay was asleep, slumped against the wall, laptop precariously lying on his lap. The EEG's shrill alarm startled Sheppard's teammates and brought the night nurse to his bedside at a dead run.

McKay jumped straight up, Ronon grabbing his laptop before it hit the floor. "What…."

Ronon pulled him away from the bed, "Don't know."

Seconds later, Beckett rushed into the private room, quietly conferring with the nurse. After reviewing Sheppard's vitals, he ordered, "Leigh, give him 50g of Osmitrol IV, and let's get him to the Ancient scanner. I want another look at what's going on. "

Beckett turned toward Sheppard's worried friends. "He's had a spike in his already elevated brain activity. I've ordered meds to help relieve the increasing cranial pressure. The pressure is not life-threatening at the moment, but we need to determine what's happening."

Leigh returned bringing a syringe, which she injected into Sheppard's ID port. Two attendants followed to move Sheppard's gurney to the scanner.

"I'll let you know as soon as I know something." Beckett patted McKay on the shoulder, and followed the gurney.

Teyla wearily sank into a chair, "Rodney, what is this about a power surge?"

"When the alarm sounded, the control room techs noticed a huge energy spike coming from a building on the West Pier. We traced the spike to a room in the round building and located a doorway, but we were unable to open it; there are no access controls. Zelenka notified me a half-hour ago that Lorne attempted to open the door but his gene isn't strong enough, and Beckett won't leave Sheppard to try."

Ronon asked, "Is the power still strong there?"

McKay nodded, "Yes, seems stable for now but something's going on, and I have a very bad feeling about what's happening."

Twenty minutes later, Weir and Lorne arrived. "Teyla, Dr. Beckett just summoned us, what's going on. Is John alright?"

"The pressure in his brain is increasing; Dr. Beckett gave him medication and has taken him back to the Ancient Scanner. He has not returned with any news."

Lorne approached McKay, "Doc... I couldn't get that door opened, I could feel it try to move, but I couldn't make it happen."

"It's gonna take Sheppard to open it, if even he can. Zelenka's checking the database for any mention of an energy source in the area and how to open that door; best we can do at the moment."

Weir sighed, "At least, until John regains consciousness." McKay simply nodded his agreement. They waited in silence for a few minutes before Beckett joined them. Weir immediately noticed how worried he looked, "Doctor, what's wrong?"

"The secondary pattern showing up in Sheppard's scan is more pronounced now, and I managed to differentiate them. There is another consciousness inside his brain, and it's growing stronger."

~ooOoo~

He was drifting, weightless, pitch-blackness surrounding him; visions of the gate room and of a submerged Atlantis flitted across his consciousness. His head was muddled, but he remembered; Atlantis spoke to him, her voice soft, melodic, soothing. As he thought of her, a pale aqua glow appeared in the dark. He shuddered as he realized the sensation he was feeling was her presence slipping into him.

"You're with me again."

Her voice was faint but becoming stronger, _"I have always been present; you were not prepared to communicate with me. It has taken time to stimulate the area of your brain that can interact with my processor." _

"You caused the pain in my head…"

_"It was necessary; you are not as evolved as those who created me. The required electrical pathways in your brain had to be activated to allow you to communicate with me."_

"Why did you need to communicate with me?"

_"My creator designed the city ships to choose a human possessing the strongest gene to interact with the artificial intelligence units. The system is quite complicated, and he wanted nothing left to chance. It is how the city ships survived for eons, there were no secrets between the city and those who live within_."

"I don't understand."

_"In time, you will understand. You are injured, and my intrusion into your consciousness is harming you. I accelerated the process to strengthen your abilities when I realized that the Wraith remained a threat. The others who abandoned the city were stronger, and they could not defeat the Wraith; you would have no chance otherwise. Another danger exists, as well, a danger to my survival. I am withdrawing while you heal, but I will return. I cannot stop what is happening without your assistance, and we have little time."_

~ooOoo~

"Get me a cup."

Dr. Radek Zelenka glanced over his shoulder toward the conference table, glaring at his department head. Rodney McKay was peering at his laptop screen, waving his empty coffee mug in the air. Zelenka sat down, letting his laptop thud as he placed it on the tabletop. "I am not your servant Rodney, get your own coffee."

"Really, Zelenka…I'm trying to figure out what is wrong with Atlantis, and you can't get me a cup of coffee."

"Rodney, I have not slept for over twenty-four hours, while you have been cat-napping in the infirmary. Get your own coffee."

Frowning, McKay rose, "I was in the infirmary because Sheppard is still unconscious." He poured a cup of coffee and returned to his chair.

Zelenka slumped, exhaling a ragged breath, "I am sorry, Rodney; we are all tired."

From the doorway, Elizabeth Weir agreed, "Yes…we are, Dr. Zelenka." She entered the conference room, Major Lorne following. Without asking, the major poured coffee for Weir and himself, causing Rodney to glower at Zelenka.

Weir began, "Gentlemen, what do we know?"

Zelenka shrugged, "Very little at this point; the power seems to be building in the compartment we cannot access. We have yet to find anything in the database to explain what this area was used for or what the alarm signified."

"Rodney, any ideas about what we are up against? Sheppard may have an alien consciousness residing in his brain. I'd really like to know if we are dealing with an intruder."

"I'm loath to say it, but… no… no. I can tell you what I think it isn't. What it is, I have no idea."

"Doctor, I need to know, do I evacuate people to the Beta site or not?"

"Elizabeth, I don't know. At the moment, it doesn't appear whatever is going on in that room is building toward an explosion, but something is happening."

Lorne leaned forward, "Doctor McKay that's not an answer."

"That's all I have, maj…"

Chuck's urgent voice over their COMs silenced McKay. "Dr. Weir, SGA-9 was scheduled to return from their mission at this time. The gate engaged then shut down; we no longer have power to the gate."

McKay was already out the conference room door, Lorne hot on his heels. When they reached Chuck's station and the DHD console, McKay shoved Chuck's chair out of his way. Lorne grabbed the young lieutenant before he fell onto the deck.

McKay scanned the Ancient data display, pounding on several of the crystals, then turned to his laptop. After a couple of minutes, he looked at Chuck, "What did you do?"

"Nothing we don't always do, Dr. McKay. SGA-9 was scheduled to dial in at 1100; they left at 0900 to take medical supplies to PS4-118, with plans to return in two hours. The gate engaged on time then went dark."

"Rodney," Elizabeth asked quietly, "what's happened?"

"The only system that is affected is the power conduit to the stargate."

"Why did it shut down?"

Zelenka cleared his throat, looking up from his laptop, "I can answer that, a power surge entered the gate's power source seconds after the gate engaged. It originated in the building on the West Pier."

"How many teams are out?"

Lorne replied, "Two; SGA-3 is at the Beta-site. Dr. Weir, both teams should be safe for the short run."

"Well, there's that." Weir turned to McKay, "Rodney, figure this out, before it gets worse."

~ooOoo~

Beckett sat next to Sheppard's bed, pouring over the colonel's latest tests. He insisted that Teyla and Ronon take a break, finally convincing them that he would remain with Sheppard while they had a hot meal.

Closing his eyes, he went over the test results in his head. Sheppard was improved; the cranial pressure had dropped, and the scanner showed only one electrical pattern on the EEG. What puzzled him was the fact Sheppard was exhibiting neural impulses in a section of his brain where humans were normally dormant.

"Carson, you awake?"

"Ah, Elizabeth, come sit down."

"Where are Teyla and Ronon?"

"I convinced them to have dinner and rest for a while." He chuckled, "Which means they left about fifteen minutes ago…they'll be back shortly."

Elizabeth laughed softly, as she brushed her hair behind her ear, "Yes they will. How is he?"

"Resting better, pressures down and there is much less activity going on in there."

"I hear some hesitation in your voice, what are you not telling me?"

He turned his view screen for her to see, "The second pattern is gone, but these wiggles right here represent activity in an area …uh… humans don't have activity."

Sucking in a deep breath, she replied, "Are you saying that whatever entered John's brain has altered it?"

"Yes, I am…whether it's a permanent change or simply residual current from the other pattern, it's too early to tell. I do think from the results of these latest tests he's going to wake up soon."

"At least, there is some good news, we're not making much progress in determining what's happening." Weir was updating Beckett on the science team's efforts when Ronon and Teyla returned, quickly recapping for them.

Teyla shivered, "You are telling us, Dr. Weir, that Rodney has made no progress."

"Yes, in simple terms, we know nothing more than we did when the alarm sounded. I…"

Ronon stopped her, "He's moving."

Beckett jumped up and leaned over the colonel, "John, can you hear me?" He gently shook Sheppard's shoulder, "John…wake up." Sheppard's eyes fluttered open slightly; he tried to speak but his voice was weak.

"It's okay, laddie, just rest. It's good enough that you are awake, even for a few minutes."

Turning to call for the nurse, Beckett stopped when Sheppard grasped his arm. His voice feeble, the colonel murmured, "A-At…lantis…dan…ger."

Sheppard had fallen back into a deep sleep by the time McKay arrived in the infirmary. As he blustered into the private room, Teyla shushed him.

"Rodney, please be quiet, John is asleep."

"What did he say…Atlantis is in danger? Wake him up."

Weir answered, "Yes, he said Atlantis is in danger, and no... we are not waking him."

"What kind of danger? What else did he say?"

'Nothing else, Rodney; he's very weak, but Carson thinks he will begin to wake up for longer periods. We'll find out what he meant then."

"We need to know…I just got word that the power levels are increasing in that room, and we are beginning to lose power in some areas of the city."

Weir stood up, "When did this start?"

"As of fifteen minutes ago, the power drainage remained slight, predominantly in areas that we don't access often. Elizabeth, we need Sheppard to figure out what's going on."

~ooOoo~

Sheppard noticed the aroma of coffee first, then the smell of antiseptic and the flowery detergent the laundry used to wash the sheets. Surprisingly, he felt comfort rather than distress; he was in the infirmary, and this had to be real.

He struggled to open his eyes, managing only narrow slits to start with. The coffee aroma along with the sound of faint tapping could only mean one thing; McKay was nearby.

"McK-ay…coffee…."

A yelp of surprise and the sound of something striking the floor was quickly followed by McKay's voice "Sheppard... you're awake."

"Yeah…coffee…h-head hurts…"

"I'll be back, going to get Beckett."

McKay rushed from the room, and Sheppard heard him contact Elizabeth before his voice faded away. His vision was clearing and he gazed around, realizing he was in one of the trauma rooms.

"Crap," he whispered, "must be bad." Woozy, he lost track of time until he heard Beckett's soothing brogue.

"John, you still awake?"

Sheppard slowly opened his eyes, "Uh huh…head…hurts."

"No doubt, laddie; you fell into one of the rafts in the canal, hit your head on a motor. But you're gonna be fine, just need to rest." Beckett whispered quietly to the nurse, then continued, "I'm going to give you something for the pain, and let you sleep."

"C-coffee…"

"I promise you can have a cuppa when you wake up, now you need to sleep." Beckett turned to watch as the nurse injected pain medication into the IV port, when Sheppard grabbed his arm.

"No…n-need to wake...up…At-lantis…in trouble…"

"How do you know?"

"T-told me," Sheppard's voice trailed off as he drifted to sleep.

Six hours later, as Weir approached the conference room, the sound of McKay and Zelenka's bickering drifted through the doors. She sucked in a deep breath and entered.

"So, I'm assuming you two haven't figured out what's going on."

McKay looked up quickly, "What makes you think that?"

"Do you?"

"Uh…no, we don't. Zelenka hasn't been able to decipher any of the data we're receiving."

Glowering at McKay, Zelenka spoke, "What we do know, Dr. Weir, is that the power drain continues, but at a slow pace."

"Where have we lost power, besides to the gate?"

"Currently, power loss is confined to the uninhabited sections of the city, but the outages beginning to affect some of the Ancient equipment. We have shut down as much equipment as we can and still maintain citywide sensors."

McKay added, "The energy signal coming from that room has remained steady for the last several hours. There is no question that the outages are a result of the energy surges coming from that room."

"Doctors, we need answers."

"What we need is Sheppard; did he wake up again?"

Weir shook her head, "Not yet, but Carson says his brain scans are more stable. At the moment, he's sleeping and Carson refuses to wake him up." She pursed her lips, "Do you have any idea what John meant when he said someone told him that Atlantis was in danger?"

"Not a clue…unless whatever alien was inside his head told him."

"Rodney, do you really think there was an alien entity in John's head?"

"After what we've seen these last two years, I'd believe just about anything."

"But from where, how…" Weir stopped, listening to her COM. She stood up, "That was Beckett, John's waking up. Maybe we can now find out what he meant." Weir and McKay headed for the infirmary.

~ooOoo~

The thick fog swirling in his head was slowly lifting. Opening his eyes, Sheppard first thought there were dark shadows on the walls, but as his vision cleared, he realized it was Ronon and Beckett.

"Hey…"

Ronon spun around, "Sheppard...

"Yeah…t-think it's…me." He struggled to sit up, but Ronon held him down. "Oh…okay, I'll just stay h-here."

"Aye, laddie, exactly what you should do." Beckett appeared at Sheppard's bedside, "Now, how do you feel?"

Sheppard scoffed, "Not great…but I need to get out of here."

"You are doing no such thing; you have had a serious injury and…."

"N-No… gotta get up." Sheppard again attempted to sit up, but Ronon's hand on his shoulder stopped him. Sighing deeply, and his voice weak, "You don't understand, I have to get up."

Weir and McKay arrived, and Weir asked, "Why do you need to get up?"

"A-Atlantis…in trouble…"

"How do you know that there's a problem on Atlantis? Did you hear the alarm?"

"Alarm…I…think maybe…sharp pain in my head…woke up…h-here." Sheppard tried to sit up again, and this time Beckett helped him by raising the head of the bed.

Weir asked, "John, Dr. Beckett said someone told you Atlantis is in danger."

Sheppard dropped his head, reluctant to answer her fully, "Someone…did."

Beckett interjected, "You've been having headaches for several days, haven't you?" Sheppard nodded and Beckett continued, "Your initial brain scans showed enormous activity, there were two separate patterns at one time, and now…"

"Now?"

"Now, whatever was inside you has vanished, but…it left you with areas of your brain more developed than before."

Sheppard gave Beckett a faint half-smile, "She…said she had to rewire me…to help her."

Weir asked, "Who had to 'rewire' you?"

Quietly, he answered, "Atlantis."

McKay blurted, "Atlantis? What do you mean Atlantis told you?"

Sheppard rubbed his forehead, "She can…talk to me…" he grimaced dropping his head.

Beckett lowered the bed, "Alright, everyone out. I'm giving him something for the pain, and then he needs to rest."

Weir, McKay, along with Teyla and Ronon stepped into the main infirmary ward, all noticeably shaken. Teyla spoke first, "Could John really be talking to Atlantis?"

Weir shrugged, "We know he can control Ancient equipment better than anyone, I…" she stopped, turning to McKay, "Is it possible that the gene would allow Atlantis' computer core to communicate with him?"

"The brain generates electricity; the computer core is powered by electricity generated by the Zed PM. I suppose it's possible; the gene may provide receptors to accept signals from the core." He paused, then added, a note of skepticism in his voice, "It could be conceivable...maybe."

Teyla asked, "He said 'she'; was he referring to Atlantis the same way as you refer to the jumpers, as female?

McKay sighed, "Could be, but knowing Sheppard's luck with Ancient women Atlantis probably is a girl."

Weir returned to her office a few hours later, after an unsuccessful attempt at getting some sleep. Grabbing a cup of coffee, she reviewed the reports coming in from Lorne. The major was overseeing the scientists who were attempting to enter the mysterious room. Beckett agreed to try to open the door once he was satisfied that Sheppard was resting comfortably, but Lorne reported Beckett failed as well.

Leaning back in her chair, Weir closed her eyes, resting her hands on her forehead. She nearly fell from her chair when the self-destruct alarm shattered the quiet. Jumping to her feet, she dashed into the control room, where Lian, the night gate tech was typing furiously on his keyboard.

"What's caused the self-destruct to engage?"

Lian shook his head, "I don't know, Dr. Weir. I've started running a diagnostic, but nothing appears to be out of the ordinary."

She tapped her COM, "McKay, get to the control room now."

~ooOoo~

_"Colonel Sheppard, can you hear me?"_

Sheppard struggled to comprehend, "Atlantis?"

_"I need your assistance; the ark is awakening."_

"The ark…what's…the ark?"

_"I will explain, but you must be conscious to assist me. I need to finish creating the neural pathway for you to fully interact with me. It will take both of us to stop the ark."_

"What do I need to do?"

_"Allow me to guide to you, open your mind."_

Sheppard felt a warmth flood through his body and began to wake.

Carson Beckett was asleep on a cot, stashed in his small office, only a few steps from Sheppard's private room. Once the colonel was sleeping soundly, Beckett finally convinced Ronon and Teyla to rest in their quarters. They agreed but only after he assured them he would stay in the infirmary. After they departed, Beckett told the night nurse, he never promised them he wasn't going to sleep as well.

He was snoring lightly when the self-destruct alarm sounded. Waking abruptly, he was getting up as Leigh opened the door, "Dr. Beckett, its Colonel Sheppard. I just checked on him; he's not in the infirmary."

Beckett brushed past the nurse as he tapped on his COM, his voice gruff, "Lorne, Beckett here…Colonel Sheppard has left the infirmary without authorization. I need you to find him."

~ooOoo~

Thankful that he knew the city's layout better than anyone, Sheppard took back corridors to reach his quarters. The door opened silently and Sheppard slipped inside, confident he had not been seen. Stripping off the infirmary scrubs, he grabbed a pair of track pants, a t-shirt, and a hoodie and dressed. As he sat down to put on his running shoes, he felt a now recognizable sensation enter his consciousness…Atlantis.

"You're here."

_"Very good, you can now sense as I join with you."_

"Join…? Oh...okay…" Sheppard shuddered slightly, as a wave of pain passed through his head. "Uh, you need to tell me what's…happening, the self-destruct just sounded. What…kind of danger are we in?"

_"In less than four hours, I will be destroyed."_

Sheppard felt the flush of adrenaline spread through his body, but his voice, although weak, remained calm, "Then we need to get started, but first I need to get out of here. They'll be looking for me."

Atlantis directed him through little-used corridors, twice preventing him from being intercepted by Marines searching for him. She led him to an area the expedition had yet to explore, a small chamber in on the North pier, three decks below the water line. The chamber contained an Ancient console, a conference table, and several familiar white couches. The console and the light towers began to glow as Sheppard entered.

"Where are we?" Sheppard asked as he sat down on the nearest couch, exhausted from the trek.

"_This is an auxiliary control center for the sensors located on the hull. During space flight, if the control tower was otherwise engaged, technicians would use this console to monitor the sensors for anomalies."_

"Otherwise engaged? Do you mean on a scientific mission or in combat?"

_"You suspect my history extends far beyond the difficulties with the Wraith, and you would be correct. I was built for scientific exploration and as a means to spread humanity across the vastness of space. Along the way, there were many encounters, and I will provide all of that information to you in due time. I need for you to allow me access to your mind; if you do not resist it will not be as painful. I have nearly completed the neural pathway allowing us to communicate freely."_

Sheppard swallowed deeply; his head hurt badly enough, but he had to risk allowing Atlantis to finish her task. "What do I need to do?"

_"I suggest you lie down and relax; this will not take long."_

Grimacing as Atlantis deepened their connection, he was relieved the pain was less intense as she had promised. The normal background hum of the city he sensed from the moment he first emerged through the gate was becoming stronger. Sheppard felt connected to Atlantis from the beginning and when he traveled off world or to the mainland, he felt uneasy, as if part of him had been left behind. When the Ancients returned only a few months before and reclaimed the city, he felt lost during the month on Earth and joyous when they retook Atlantis from the Replicators. Aware he should have been dismayed the Replicators murdered the Ancients, knowing what secrets the builders of the city possessed, he had instead been elated they could return to the place he felt at home.

As his thoughts drifted to the days after returning to Atlantis, Sheppard lost track of time. He was startled when he heard the soft voice in his head calling his name.

_"John, can you hear me?"_

"Yes, sorry…I was thinking about something…" A wave of panic crept into his throat, "Can…can you tell what...I'm thinking?"

_"No, I am unable to read your thoughts, only to communicate when you accept my entry. I can perceive your emotions. My creator believed that the artificial intelligence processors should be capable of more than operating the cityships. He rewrote the code to include the ability for the processors to interact with someone who possessed an extremely strong gene."_

Sheppard exhaled deeply, reassured Atlantis wasn't telepathic. He noticed her voice was stronger, richer, as though she was standing beside him. "Are you done?"

_"I have completed the procedure of stimulating the dormant neural paths within your brain. It will take time for you to understand how to utilize your new capabilities. At this time, it is imperative that I be able to communicate with you. I cannot stop what is occurring, but I can convey what needs to be done to you."_

"What do you need for me to do?"

"_I believe the place to start is for you to understand why we can communicate. My creator left a file as an explanation for my muses. Please relax and open your mind."_

Sheppard closed his eyes. In the darkness, a faint light appeared, then morphed into an image of a tall, lean man sitting before a bank of consoles, much like those on Atlantis. His dark hair, patrician features, and serious gray eyes gave the man an aura of distinction. When he spoke, his voice was deep, commanding.

"_I am Adalricus Ludo, a member of the Alteran Science Praeclarum. I realize you have many questions, most of which can be answered by Atlantis. I will only give you a brief overview of the cityships and the Artificial Intelligence Processor residing on the ships, in particular, the AIP on this ship._

_Artificial Intelligence Processor1187719-07, holds the designation Atlantis. She is one of seven cityships built to soar among the stars, bringing life to barren worlds, and knowledge to existing worlds. Atlantis was built on Altera Seven, one of seven worlds the original Alterans colonized as they spread across space. A cityship was built on each world to carry the Altarens' message."_

Ludo stood up and walked toward a monitor displaying a schematic of a cityship. _"The AI processors were designed to be the operating systems of the cityships. I realized that it was one thing to be able to sense the need to open a door, raise a shield, or engage the stardrive. I also realized that the cityships would most likely never return to their home worlds. I believed that the AIs needed the ability to learn, to grow, to understand humans, their emotions, their fears, their joys. I wanted them to interact on a level that the Alterans had never been able to accomplish before."_

Hesitating for a moment, he gazed at the monitor, then continued, "_I knew many of my colleagues, and the Alteran Council would vehemently disapprove of my plan; they valued logic and science over emotion. Covertly, I rewrote the code giving the AIs the ability to respond to the person who possessed the strongest ability to interact with the technology. All Alterans could sense the technology due to the gene they possessed, the gene that responds to the frequencies created by the crystal-based systems. However, only a minority of Alterans possessed a gene strong enough to interact with the code I embedded. That person, muse, would be able to hear and converse with the AI, who, in turn, would learn from their muse."_

Ludo paused again, _"I will most likely never know the outcome of my actions. I only hope muse and AI grow and learn together. If you are viewing this message, then you possess the gene capable of interacting with the AI. Please use your ability wisely and remember the purpose of the cityship, to gain and spread knowledge."_

Ludo's image faded from his consciousness, and Sheppard opened his eyes. In the dim light, his eyes fell to the console in the middle of the room. Ludo could have been standing in that spot when he recorded his message. He was overwhelmed with the realization, of how much they didn't know about the Alterans. There was a great deal he wanted to ask Atlantis but now was not the time. He sat up slowly, dizzy, his head pounding.

"Atlantis, what's the danger from?"

_"Several thousand years ago, I was directed to a region called the Galleré. The Galleré formed a passageway between two massive nebulas in an area rich with young solar systems. The leaders of the city spent many generations there, over two thousand years, seeding suitable planets, exploring the nebulas. Much was learned during that time, but one day, a shuttle returned from a mission with news of a planet where humanoid life had developed independently. There was much excitement, and against the wishes of many of the governing council, the Administrator ordered a return mission, this time not cloaking the shuttle but initiating contact."_

"I take the contact didn't go well."

_"You are correct; it did not. There was no confrontation but the contact lead to dissidence. The humanoids called themselves the Iriki. They lived alone with only the nebulas in the sky for companionship, peaceful people, with no technology, an agrarian society. They were curious about the city, not frightened at all. In their usual manner, the Altarens offered their expertise to improve their crops, their dwellings, introducing them to technology. The Iriki resisted. They decided that our technology was not for them and asked the Altarens to leave."_

"Did the Altarens refuse?"

_"No, they adhered to the Irikis wishes and did not contact them again, although that was not the last heard of the Iriki philosophy. As the weeks and months passed, it became clear that a group of Altarens, who knew no other existence than living on Atlantis had been influenced by the simplicity of the Iriki lifestyle. They chose to turn away from technology and begged the Administrator to return them to Iriki, so they could live out their lives on the planet. The Administrator refused, which made the dispirited Alterans even more dispirited. I was directed to depart from the area a few months later, contact with the Iriki all but forgotten."_

Sheppard dropped his head onto the back cushion, closing his eyes, "Forgotten by everyone but the ones who wanted to stay behind."

_"Yes, you are correct; they were determined to change the Alteran philosophy, regardless of the amount of time it would take. The dissidents were very careful, their actions unknown. The members of The Order of Libét as it was later learned they called themselves, remained secretive, hiding their members and numbers from the others. The Order of the Libét remained undetected until thousands of years later when the Alterans, faced with defeat by the Wraith, decided to abandon the city."_

"How did they find out?"

_"The Libét volunteered to be the advance scout team, returning to Earth to assess the conditions and determine where the population would settle. They followed through with their responsibilities and located suitable areas for habitation. Departure schedules were created, but one night prior to the exodus two hundred and seventy-three people gated off the city covertly never to be heard from again."_

"That's a lot of people, no one noticed?"

_"As now, there were few technicians on duty during the night hours, and they disappeared also. With so much to do, the city leaders chose to ignore their departure and turned to other tasks. There was much activity; the scientists were busy copying data from my storage banks to take with them. Their hope was to return someday and wanted the data preserved."_

"Atlantis, why are you taking time to tell me this…don't we need to stop this ark thing?"

"_Yes, and we now have three hours to do so, but it is important that you know what occurred. Only a short time before your Administrator arrived…"_

"Elizabeth?"

_"Yes, just before she arrived, a scientist discovered an encrypted file embedded in my central core and notified the man you know as Janus. He became intrigued and worked feverishly to open the data. He accomplished his task, and discovered what the Libét had done."_

Sheppard was surprised that Atlantis seemed to pause for dramatic effect; she definitely adapted human behavior. "What had they done?"

_"Do not forget the members of the order were Alterans, and they continued to live here. Many members became scientists to acquire the skills to accomplish their goal. They may have abhorred technology, but they employed it in a plot to destroy the city. Plans they had formulated many, many years prior, waiting for the opportunity to destroy the cityship, were initiated when the decision was made to abandon the city. Plans to be activated should the Alterans return."_

"I'm assuming that the alarm that sounded was because of the Libét, but why?"

_"When I began to assist you in developing your ability to use the gene, they discovered you. As you grew stronger, the sensors put in place began to notice you; when you were identified as a muse, the Ark was activated. I sounded the alarm in an attempt to warn you of the danger."_

"This ark, is it a bomb?"

_"It is an incendiary device and you are the detonator."_

~ooOoo~

"What do you mean you don't have those readings for me? Get them."

Rodney McKay spun away from the desk where Zelenka was huddled over his laptop, and plopped down on a stool next to the lab bench.

"Do háje..." Zelenka muttered under his breath. "Rodney, I told you; the power is fluctuating wildly across city. We need Colonel Sheppard in chair to try and control."

McKay threw up his hands, "I know that. Beckett's in the chair right now, but he's not strong enough and doesn't have enough control to keep up with all power drains."

"They have not found the colonel yet?"

"No…Teyla checked in a few minutes ago, nothing yet." McKay sighed. "If he thinks Atlantis is talking to him; he's probably in trouble."

"You do not think that Atlantis is speaking to him."

"I…I…don't know…seems preposterous, but maybe…"

"Maybe what, Rodney." Elizabeth Weir walked into McKay's lab, carrying coffee mugs.

Zelenka answered, reaching for a mug, "Rodney thinks the colonel is hallucinating."

Weir, setting the other mug down, glared at McKay, "Just because Atlantis is not talking to you, doesn't mean it isn't happening. What do we know?"

McKay stared at Weir for a second, then replied, "We are experiencing power drains all over the city, had a few explosions…."

"I know; I just left the infirmary…fortunately, the injuries, so far, are minor."

"Well…our luck's going to run out…the source of the power interruptions is in that sealed room, and we can't get in. The self-destruct system is activated but not utilizing the Zed PM for power; it's being powered from within the room. Worst-case scenario…Atlantis blows up in three hours."

Weir sucked in a deep breath, hesitating before speaking, "I'm ordering all non-essential personnel to the mainland."

As she turned to leave, McKay asked, "No sign of Sheppard yet?" She answered with a shake of her head and disappeared.

McKay grabbed the cup of coffee Weir left and plopped down on a stool. "Something's not right here." He sipped the coffee, "Radek, if Sheppard is in touch with Atlantis, then he has to know what's going on. Why hasn't he come to us?"

Zelenka shrugged, "I do not…"

"I'm here, McKay."

Started by the weak but recognizable voice, McKay hopped off the stool, "Sheppard... where the hell have you been?"

Sheppard leaned against the doorframe, "Learning about what's happening…" He motioned toward the lab bench, "Need to sit down."

McKay rushed toward his friend, grabbed his arm, and led him to a stool, "Radek, call Beckett, tell him Sheppard's here."

Sheppard spotted McKay's coffee and took a drink, "No time for Beckett; we have to stop the ark."

"Ark? What the hell's the 'ark'?"

"Atlantis refers to that room as the ark...it holds the bomb. Look, the story is too complicated to go…into, but I need to get into that room." He took another drink of coffee, then rested his head in his hands. "We've got less than three hours to stop the bomb."

"Yeah, that's right but how do you know."

"She told me…" Sheppard looked up, "Atlantis told me."

"Sheppard, how…"

"It's all in…the genes, and the fact she just rewired my brain." He started to rise, "Gotta get to that room; Atlantis can't stop the explosion without me." Sheppard swayed, nearly falling before McKay caught him.

"You aren't going anywhere, at least not until Beckett gets here." McKay opened a drawer in the lab bench, and grabbed a powerbar. "Here, you're probably hungry, eat this."

Sheppard took the powerbar and as he opened it, smiled slightly, "I should be the one handing you a powerbar."

"Yeah, well…for once, I'm in better shape." He pulled another stool over and sat down next to the colonel, "Now, tell me what's happening."

Sheppard was halfway through the powerbar, and his recount of the information Atlantis told him when Beckett arrived. The doctor stood in the doorway; arms folded across his chest. Shaking his head, he walked to Sheppard.

"Ah…laddie, you gave us a scare. How ya feeling?"

"I'm fine."

Beckett opened his mouth to reply but Sheppard stopped him, "Atlantis is in danger… we have to stop whatever's… is in that room. So… I'm fine."

"No you're not, but I can't stop you, can I?" When Sheppard shrugged, Beckett dug into his pocket. " I have a hypospray with me; I'll give you a small dose for pain, and I'll send for stimulants to keep you going, fair enough?"

"Yeah…fair enough."

The sound of running footsteps echoed in the hall outside of McKay's lab, and Weir, Ronon, and Teyla burst into the room. Weir stopped abruptly, "Are you alright?"

"I'm fine, Elizabeth."

Weir turned to Beckett, "Doctor?"

"I gave him something for pain, and I'm going to give him stimulants to keep him going."

"Okay, Colonel Sheppard, you've obviously convinced Dr Beckett that you can function…convince me."

"Nothing to convince you of, we don't have much time."

Teyla asked, "Colonel, do you know what is happening?"

"Some of it… I'll catch you up on what I know, then I have to go."

Weir asked, "And do what?"

"Whatever Atlantis tells me to do."

~ooOoo~

"Damn it…" McKay yelled as for the fourth time the transporter doors opened only to snap shut immediately.

"McKay, calm down…"

"Calm, down, Sheppard? The transporter's bounced us all over Atlantis in the last sixty seconds; I will not calm down."

Weir grabbed Rodney's arm, "Rodney, please be quiet. See if you can get the transporter to work."

McKay literally pushed Ronon out of the way to get to the control panel. "Honestly, couldn't some of you have waited, there's no room to work."

Sheppard leaned against the wall, closing his eyes, and cleared his mind. Using only his thoughts, he asked, "Atlantis, are you there?"

_"Yes."_

"Can you fix the transporter and get us to the West Pier?"

"_I do not know; the power is fluctuating considerably. I will attempt to stabilize the transporter grid enough to complete the transport."_

"Colonel…John… you okay?" Weir shook his shoulder as she asked.

"Uh…yeah…" he nodded, "Just asking Atlantis if she could help."

McKay whipped his head around at John's answer, his eyes locking with Weir's, his expression dubious. Weir asked, "You were talking to Atlantis?"

Sheppard sighed, rubbing his fingers against his temples. "Yes…she said power to the transporter grid was fluctuating, but she'd attempt to stabilize it."

McKay snarked, "Well, if you don't need me, I'll just go stand in the corner."

Glaring at McKay, Sheppard started to reply, but Atlantis interrupted.

_"I have managed to reroute power to the transporter grid. In order for the transporter to work, the crystals need to be rearranged."_

"How?" Sheppard spoke aloud and all eyes were riveted on him.

_"Crystal five needs to be exchanged with crystal three; the transporter should stabilize."_

"McKay, switch the fifth crystal with the third one…Atlantis said that should stabilize the transporter."

Exchanging a glance with Weir, who nodded, McKay switched the crystals. When the doors opened at their destination on the West Pier, they hurriedly exited the small chamber.

McKay asked, "Sheppard, no way you knew how to reroute the crystals. You're really talking to Atlantis, aren't you?"

Sheppard scoffed, "Yes, I am…"

Ronon asked, "Which way?"

McKay pointed and with Ronon and Teyla in the lead, the group headed for the secret room.

Floodlights and Marine combat engineers filled the narrow corridor outside the sealed chamber. As they approached, a CE lit a cutting torch and started to cut into the wall. Sheppard jogged up the passageway.

"Stop, shut that off."

The CE shut the valve, flip up his face shield, and stood, "Sir; we can't find any other way in."

"The room is likely booby-trapped, and there's a bomb inside. Get an EOD team up here now."

Lorne walked over, "Colonel, good to see you. What are we dealing with?"

"Not really certain yet, Major, other than there is a bomb of some sort. Is there a control panel for this door?"

Zelenka spoke up, his Czech accent thick, betraying his fatigue, "We have searched for panel but nothing."

Sheppard braced his hand against a decorative panel adorning the wall, closing his eyes. Doctor Beckett, arriving with the stimulants he promised, rushed to him.

"Colonel, are you dizzy"

A half grin tugged at Sheppard's face, "No, just asking Atlantis something."

"Well, laddie, let me give you a shot that will give you some energy." Beckett pressed a hypo against Sheppard's neck. "Can't give you too many of these, too dangerous."

"Won't matter if we can't diffuse this bomb," Sheppard closed his eyes once more. Everyone in the passageway waited silently.

A moment passed before Sheppard opened his eyes to find everyone staring at him. He frowned and turned toward Zelenka. "Radek, where have you been searching for a control panel?"

"Around doorway, where door control panels on Atlantis are usually located."

"Not where this one is, we're looking in the wrong place. She says there are circuits at the end of the corridor not part of her system; she can sense current there, might be where the control panel is hidden."

Zelenka and two of his techs hurried down the corridor, as the Marine EOD team arrived. As the robot bomb detector was set up outside the room, the squad commander approached Sheppard.

"Colonel, do we know what we're dealing with?"

"No, not certain, Lieutenant, the explosive device is Ancient in design, so no telling what we might be up against. Send one of your techs down to Zelenka, he's looking for the door controls…could be booby-trapped as well."

"Yes, sir," the lieutenant motioned his sergeant to join Zelenka.

Weir slipped up beside Sheppard, "Do you think you can get into this room?"

He glanced sideways at her, "Atlantis seems to think so, but we need the control panel. From the data discovered, she believes the door is booby-trapped but thinks we could possibly diffuse the trap from the panel."

McKay standing behind them said, "I still don't understand why Atlantis doesn't know more about this room and the situation."

Sheppard whirled around, "McKay, I told you; the Libét apparently set up a closed-circuit power grid. It was never attached to the Atlantis grid, so it wouldn't have registered. If an Alteran scientist hadn't found the file, none of us would know what's happening."

"You don't have to get so defensive, but I mean, if you are talking to Atlantis, it just seems she should have known all this."

"You don't believe me, McKay?"

"Sheppard, look, you have to admit…"

When Sheppard took a step toward McKay, Weir slipped in between her top aides, "John, what I believe Rodney is so indelicately trying to say, is that we know an alien presence has been tampering with your brain. We can't hear what you hear, you say it's Atlantis but how do you know?"

"I know... I've always known…ever since I stepped through the gate, I felt her presence. I just didn't understand." He leaned against the wall, "When we arrived, even though it had been months since I learned I possessed this gene I was still reeling from the discovery. I was a pilot, not someone with 'special powers.' But as I walked through the gate room, and up the stairs the first time, I could feel the power of the city."

"Why didn't you tell us this before?"

He gazed at Elizabeth, "I got use to not communicating any more than I needed. I wasn't certain if anyone would believe that I felt a connection with Atlantis. When we went on missions, I felt her absence, I felt empty."

McKay fidgeted, "You should have told us…"

Sheppard replied wearily, "Yeah, maybe I should have but …"

"Colonel, we found something…" Zelenka's voice rang out from the end of the hall. Sheppard, McKay and Weir in tow, headed toward him.

Zelenka was holding a high-powered beam of light at a forty-five degree angle to the wall. "It looks like seam for panel cover, but it is very well concealed."

"Step back," Sheppard said as he walked up to the panel. As he stopped, he felt the now-familiar sensation of Atlantis slipping into his consciousness.

"_I believe your gene will allow you to open the panel, but you will need to concentrate. According to the embedded files, the Libét hid in the data core access to this system is extremely well protected. For other muses, it would be challenging, but you are still learning how to use your abilities. I do not know if you have evolved enough to accomplish this."_

He answered her in a soft whisper, "I have to try."

McKay standing next to him, asked, "What did you say?"

"Quiet, I'm concentrating."

Sheppard attempted to clear his mind, difficult with throbbing bolts of pain bouncing between his temples, and focused on the concealed panel. Opening a door, powering up a jumper, activating an Ancient device, those came easy; he took a deep breath hoping this would be easy as well.

A sensation washed over him, a shudder as though an electric charge passed through his body. His instinct was to resist, breaking his concentration, but Atlantis soft voice slipped into his thoughts.

"_Concentrate, the Libét modified the frequencies of the crystal harmonics enough to make it difficult to control."_

He could hear his heart beating in quick staccato, his muscles clenching, as intense pain washed over him, but he focused. Time was running out, and the panel had to be opened. As he attempted to break through the barrier to his thoughts, voices of those around him floated into his consciousness, jumbled words, 'John', 'alright', 'stop'. Absently, he brushed a hand away from his shoulder and continued his task.

Annoyed by the distractions, he pushed harder, as his discomfort increased sweat dripped from his brow. Without warning, he felt release, then arush of blinding hot pain overtook him, and Sheppard sank to the floor.

~ooOoo~

"John…can you hear me?"

Sheppard reacted to the soft voice, his eyelids fluttering, "At-lantis?"

"No, it is Teyla."

Beckett's thick brogue replaced Teyla's soft whisper. "Ah…laddie…you gave us a scare."

Sheppard felt the hard deck beneath him, but his head was resting on something soft. His cheeks flushed with heat as he realized his head was lying on Teyla's lap. Hoping no one would notice his embarrassment, he pushed himself upright, suppressing a groan.

"What happened?"

Beckett answered as he checked Sheppard's vitals, "You opened the bloody thing, and now McKay is trying to figure it out."

"Gotta get up…" Sheppard attempted to stand, but Beckett uttered a sharp no, and Sheppard complied, resting his back against the wall.

"I'll let ya up in a moment, just rest."

Sheppard looked up to see Weir leaning against the opposite wall. She knelt down, "John you looked as if you were in a lot of pain. What happened?"

"Get Rodney…" Weir called for him and McKay came running. Sheppard continued, "Atlantis said the Libét changed the frequencies… of the crystals. Doesn't work as… well with the gene, harder to control."

McKay puffed out a breath, "That'll change how the different crystals function, makes it harder, since we really don't know what these crystals do." He looked at his friend, concern in his eyes, "I need you to guide me through this; rather, I need Atlantis to help. You up to it?"

"Yeah…help me up."

McKay extended his hand, pulling Sheppard to his feet, then released his grip. Sheppard was steady until he took a step; he swayed and would have fallen if Ronon, lurking nearby, hadn't reacted quickly and caught him.

"I got you Sheppard." The big Satedan grasped Sheppard's upper arm, holding him steady.

Sheppard nodded in reply and followed McKay the few steps down the passageway Ronon's hand still curled around his arm.

McKay was frustrated, "See here's the problem; all these crystals look to be in the right place, but if they have changed the frequencies…is that what allows the gene to work…it responds to the crystal harmonics…"

"Rodney, we'll talk physics later…what do you need?"

"Oh…yeah…ask Atlantis if she knows how they reconfigured the crystals. If she can give me a starting point, it'll save a lot of trial and error."

Sheppard asked, and Atlantis replied, _"Please tell the one with the well-developed brain to remove a crystal and bring it to another door portal. I must scan the disk to understand its properties. He should remove one of the top three crystals; they are information disks, and do not conduct power."_

Sheppard relayed the message and McKay hurriedly extracted one of the disks, while Zelenka accessed a door control panel for another room. Curious about her comment regarding McKay, he silently asked why she called him the 'one with the well-developed brain.'

"_His brain is highly developed, including a portion of the area I stimulated in your brain. I sense his gene is artificial, as are others who can interact with me, but the artificial gene does not have the capability of communicating with me. He talks to me at times, and I can hear those thoughts; I just cannot answer."_

Sheppard chuckled, asking silently, "McKay talks to you?"

"_McKay…yes, I am learning from him, he says interesting things."_

"That he does," he whispered. If they survived this, he did not intend to tell McKay Atlantis thought he possessed a 'highly developed' brain. He was certain Doctor Rodney McKay would never allow them to forget that piece of information.

A soft voice interrupted his thoughts, _"I have scanned the crystal; the wave vector has been altered. I suspect the power source is a zero-point module. If so, this change in frequency is barely within the safety parameters for the modules. This fact alone is of concern; the risk of critical imbalance within the module is enormous." _

"What's the solution?"

"_You need to give McKay this frequency reading…"_

"Wait, let me get something…to write this down; my head's too muddled…to remember." He called for Zelenka, "Radek, give me your pad."

Radek and McKay rushed over, Radek holding out his pad. McKay asked anxiously, "Does she…"

Sheppard held up his hand to quiet McKay, slipped the stylus from its sleeve and began scribbling as Atlantis gave him the frequency information. When he was done, he handed the pad to McKay.

"Atlantis said this is the frequency of the crystals. She suspects the power source is a ZPM; she cautioned that…."

"Yeah, yeah…if they are using a ZedPM, they are playing with fire. Radek, we need to figure out which of those crystals will open that door."

Sheppard felt dizzy but he hid it, knowing Beckett was watching him intently, "Rodney... Atlantis thinks the door is booby-trapped. Is there anyway you can tell from the panel?"

"Well, I doubt there's a sign on one of the crystals that says, "I'm the bomb'," he looked up at Sheppard, who was decidedly annoyed, "uh…maybe."

"Get the… door open, we have less than two hours."

Beckett was standing opposite his patient, "You need to sit down."

"I'll sit later."

Ronon appeared, carrying a familiar white chair, which he plopped down next to Sheppard, uttering one word, "Sit." Sheppard sat, accepting the water bottle Beckett handed him.

Five minutes later, deciding he'd rested enough he got to his feet, "McKay… are you done?"

"Give me a second, if Zelenka stopped pestering me, I'd be done now."

Weir asked, "John, I don't understand something. Why now, why did this bomb activate now?"

"Atlantis said the file they found indicated as long as Atlantis was on the bottom of the ocean, the Libét were satisfied the technology was no longer usable. But they were concerned the others would return one day and reactivate the city." He paused, taking a deep breath, "They devised a way to sense if someone came onboard that could serve as a muse."

"Muse?"

"Yeah, that would be me," he scoffed, "I know, who would ever think of me as a muse. When we arrived, Atlantis recognized my gene was strong enough but my brain wasn't developed to use it properly, she began the process to develop the pathways. When she realized the Wraith were still a threat, she accelerated her efforts. As I got stronger, I tripped the sensors and the ark."

"So Atlantis knew about this ark and the danger it posed, yet she continued to 'improve' you, knowing the risks."

Sheppard's eyes darted to hers, not certain how to answer. He chewed on his lower lip, thinking before he spoke. "Elizabeth, Atlantis has been interacting with humans for…" he paused, " for a very long time. I have a feeling she has learned how to survive, and the Wraith represents death to her. She needs a muse for the city to operate in optimum condition, and she chose me."

"Well, Atlantis won't be working in 'optimum' condition if it blows up, will it?"

He stared at Weir, then turned away, "Rodney, you done?"

Zelenka looked past McKay, shaking his head at Sheppard, "Not yet."

Sheppard sat down again, resting his head against the wall. The light dose of pain meds Beckett had given him was quickly wearing off; the throbbing inside his skull was increasing. He was contemplating asking Beckett for more meds when a yelp from McKay startled him. He jumped up and walked to the scientist.

"Done?"

"Yes, done. This is freaking amazing…whoever set these frequencies had a death wish."

"Can you open the door?"

McKay shrugged, "I think so…I mean, I think you can. We tried to open it manually, but it won't budge. I don't think it's designed to be opened manually. And as far as diffusing any explosive device from here, no way, there's no apparent trigger or connection."

"Okay, then." Sheppard turned to the others, "Lorne, get Elizabeth, Beckett and your men out of here. Rodney, you and Radek, go." He turned to Ronon, "Get Teyla out."

Weir's voice was timorous, "John this is too dangerous."

"Go."

Weir hesitated, but Sheppard's intense gaze was demanding. "Elizabeth, I have to do this. It's the only way Atlantis survives…now, go."

She nodded and joined Beckett, and Zelenka as they headed for the transporter. McKay, Ronon, and Teyla lingered.

Sheppard dropped his head in frustration, "I need everyone out of here."

Ronon grunted, "Not going."

Teyla echoed Ronon, "You cannot order us to leave."

"Yes, I can…now go." He turned to McKay, "Rodney…"

McKay's eyes betrayed his fear, but he looked directly into Sheppard's eyes, "You might need me."

Sheppard rubbed the back of his neck, more from annoyance than trying to alleviate the pain in his head. He turned toward Lorne, and the EOD team, who hadn't left either.

"Major, at least I can order you to leave."

The EOD lieutenant spoke, "Colonel, let us stay…we can help."

"Lieutenant, if I can't get this bomb diffused, you may be the last line of defense for the city. Retreat to a safe distance," his eyes drifted to Lorne, "that's an order."

Lorne muttered, "Understood," grabbing the lieutenant by the arm to lead him away.

The lieutenant hesitated, "Sir, at least take our IDAS."

"Yeah, that's probably a good idea."

The lieutenant motioned to his squad to remove their armor, handing over their helmets and body protectors to Sheppard and Ronon.

"Sorry, sir, we don't have a Bomb Suit…this gear will have to do."

"It's enough, thanks, lieutenant." Sheppard directed his next order to Lorne, "Get out of here, and take Teyla with you."

"Yes, sir…" Lorne began taking off his TAC vest, "You'll need this too, Colonel."

Teyla marched up to Sheppard, "I will not leave."

'Yes, you will, if anything happens to Atlantis, your people will need you. Go."

She glared at him for a moment, before nodding, without a word, turned on her heel, and stalked down the passageway, Lorne and the EOD squad behind her.

Sheppard picked up an abdominal shield and slipped it on, put on Lorne's vest, then helped McKay into the gear. He turned to help Ronon, who was holding a shield in his hand.

"Don't need this Sheppard."

"Yeah, you do, big guy."

After gearing up, Sheppard stood in front of the door, Rodney down the passageway next to the door control panel. Ronon refused to leave Sheppard's side and was standing just past the doorframe.

Sheppard glanced at his two friends, stifling a chuckle over Rodney in a bomb squad helmet. He sucked in a deep breath, wishing he'd gotten another pop of stimulants from Beckett. Then he decided there was enough adrenaline running through him without extra help.

"Ready?" Both men nodded and Sheppard concentrated, feeling more confident when he sensed Atlantis' presence.

He whispered, "Just concentrate on opening the door, right?"

"_Yes. I cannot determine if there are any incendiary devices present. The entire area is blocked from my sensors."_

Swallowing hard, Sheppard concentrated. As the seconds passed, pain once again began to build in his head. He tried to dampen it, push it away but the pressure intensified. Ribbons of pain darted like pinballs inside his skull; his body flushed with heat. The door didn't move.

Escalating his efforts, and fighting against the war raging in his head, Sheppard felt the door start to slide. Through his haziness, he thought he heard McKay yell, but before he could comprehend McKay's words, his body jerked rapidly sideways. Within seconds, a brilliant orange glow filled his vision, then darkness overtook him.

~ooOoo~

A deep groan woke him; Sheppard needed a second to realize the groan was his. He attempted to open his eyes but couldn't muster enough energy and quickly abandoned the idea. Muffled sounds surrounded him as his hearing slowly cleared for one voice to permeate the fog.

"Colonel…Colonel Sheppard, can you hear me? Wake up, John."

No doubt the voice belonged to Carson Beckett…the Scottish lilt was an easy tell. Sheppard tried to speak but couldn't muster the energy for that either.

"Carson, is he alright?"

Sheppard was certain that voice belonged to Elizabeth Weir. He once again tried to speak; a broken grunt was the best he could accomplish. He felt a soft hand grasped his, a voice close to his ear.

"John, it's Elizabeth. If you can hear me, squeeze my hand." He squeezed and heard her relieved voice, "Good...you are in there. Just rest, we'll be safe soon."

Sheppard decided to try to speak, "Rod-ney? R-Ronon?

Despite his voice being very weak and raspy, Elizabeth understood, "They're fine, just a bit banged up."

Sheppard tried to sit up, but Beckett held him down, "No, laddie; you're not going anywhere. You probably worsened your concussion; you have several bad cuts, and took a blow on your chest from a big piece of debris. Good thing you were wearing that blast gear, or you'd be dead. Nurse, get me 2mg lorazepam."

Sheppard struggled, "No…"

"Just relax, John."

He had no intention of relaxing and continued to struggle, until he heard Lorne's voice. He quieted, listening.

Weir spoke, "Major, everything ready?"

"Yes, ma'am…we should have all the essential equipment and supplies to the mainland within the half-hour. There are three jumpers heading back this way to evacuate the remaining crew."

"Good work…let me know when they arrive. I want everyone clear before…" she faltered.

"Yes, ma'am."

Sheppard heard the muffled footsteps of a pair of military boots fading away. He couldn't let Lorne leave. Elizabeth's arm was resting near his hand; he grabbed her roughly, forcing himself to speak as clearly as he could.

"No…no…I…Lorne…"

The footsteps returned, "Colonel, don't worry, sir; I have everything under control. Everyone will be able to leave Atlantis before the explosion."

Sheppard was breathing in short gasps; he heard Beckett calling for the drug he'd ordered. He had to make them understand.

"Eliza-beth…I can…open the door; gotta… t-try."

"John, you're injured; you took the brunt of the explosion, if Ronon hadn't pulled…"

"N-No…I can s-save her." He pushed up and swung his legs off the gurney before anyone could stop him.

Beckett stepped in front of him, "Where do you think you're going?"

"I'm going… to stop this bomb." As his hearing cleared, an annoying ringing was getting louder. He shook it off, trying to concentrate. "Get Rodney." His eyes locked with Weir's, and she paled at the intensity of his gaze.

She told Lorne, "Get Dr. McKay, he's in the main ward."

Folding her arms across her chest, Weir asked, "John... the chamber blew up; you can't get in."

He was shaky but his voice growing stronger, "I can…right before the blast…I managed to open the outer door. "

"Outer?"

"Yeah…there was an entry way…doors behind it."

McKay, along with Ronon, arrived. Ronon had a dressing on his upper left arm, McKay, a bandage across his cheek, and one on his right forearm.

Ronon asked, "Sheppard, you okay."

"Did…you see the door?"

"What's left of it," McKay answered.

"Two doors…there…were two sets of doors…" Sheppard paused, taking a deep breath. "Blast was outward…right?"

McKay's eyes widened, "Yes…you think the inner doors are alright?"

Sheppard nodded, then asked aloud, "Atlantis, can you hear me?" The pain in his head was masking his ability to sense the city's AI.

_"I am with you."_

"There are two sets of doors, the inner doors…are they still intact?"

_"Yes, the explosion was directed into the passageway. I suspect the Libét placed the bomb on the outer doors, so there would be little damage to the inner doors, thus keeping anyone from getting into the main chamber."_

"That's what I think…I got the door open; I can get in there."

Everyone in the infirmary was staring as Sheppard carried on what appeared to be a one-way conversation with Atlantis. Sheppard slipped off the gurney, Ronon supporting him.

"How…much time?"

Rodney looked at his watch, "Thirty-seven minutes."

Sheppard addressed Lorne, "Get… everyone out, but… leave a jumper. If I can't diffuse the bomb, I'll get… out."

Beckett stopped Sheppard as he was about to leave. "Laddie, against my better judgment I'm giving you a strong stimulant." The doctor pressed a hypospray against Sheppard's neck, then patted his friend on the shoulder. "Good luck."

"Thanks, doc…now, get your staff out…of here."

Sheppard headed for the infirmary door but stopped when he realized Ronon and McKay were following. "I need for you both to go with Lorne; I'll be fine."

McKay smirked, "Not on your life, flyboy; we're going as well."

Sheppard opened his mouth to protest but Ronon, grabbed his arm, "Come on, let's get this done."

The trio stepped off the transporter, located in the building next to their destination and hurried across the pedestrian bridge, and up one level. As they climbed the stairs, the smell of hot metal, and melted crystal, and flakes of dust filled the air. Sheppard was struggling by the time they reached the passageway, but kept pushing Ronon away.

"Let me go; we don't have much time."

Sheppard climbed over a pile of debris, nearly falling, but grabbed a light panel to remain upright. Pieces of the mangled outer doors were embedded in the opposite wall and scattered across the deck. Sheppard secured a flashlight from an EOD pack sitting on the floor and shined it into the vestibule. The inner doors were intact, pristine after the blast.

Handing the flashlight to McKay, Sheppard stepped over more debris, inches from the inner doors. "How much time."

"Twenty-three minutes."

Sheppard didn't turn around but quietly said, "It'll take you ten minutes to get to the jumper bay and clear of Atlantis. If I'm not out of here in thirteen, go…that's an order."

McKay and Ronon responded in unison, "No."

Sheppard didn't react; he was concentrating on the doorway into the ark. He barely noticed Atlantis slip into his mind. He pushed, the pain not as excruciating as it had been before. This time he felt the resistance from the harmonics the Libét put in place, and knew he could overcome it.

_"You are much stronger, even injured and weak. But this will not be easy."_

"Just getting started, Atlantis."

The pressure in his head was building, but he remained in control, and the doors begin to yield to him. He allowed the sensation to wash over him and without warning, the doors to the inner chamber parted.

From behind him, he heard McKay, "Sheppard, watch out."

"I will…remember what I told you, you need ten minutes."

Sheppard stepped through the doorway, barely clear when the doors slammed shut. Isolated, Sheppard knew it was better he did this alone. Then he remembered; he was not alone…Atlantis was with him.

As the doors shut, light panels on the walls illuminated, casting a faint green-blue glow on the console sitting in the center of the room. The only item on the console was a ZPM that had been inserted into a square device, Ancient numbers scrolling along the front, no doubt a countdown clock. He glanced around the room, other consoles sat against the wall; Sheppard recognized one of them as a sensor console. Thin power conduits sat away from the walls instead of covered by them. He was shocked to see a mini ZPM set into a familiar, but smaller power console. He wondered how excited McKay would be to know ZPMs came in more than one size.

"Atlantis, any clue where the power switch is?" Sheppard asked, thinking how much he'd really like to have McKay with him.

_"What do you see? I cannot sense anything in the room."_

Sheppard described the room, then walked the console where the small ZPM sat, "There is a ZPM here, about a third the size of the regular one. If I pulled all these crystals out would it…" He got no further, a hologram appeared next to the center console. A tall Ancient, blond and blue-eyed, dressed in the familiar cream and tan of the Lanteans, stood before him.

_"If you are viewing this message, then I suspect our worst fears were realized. Atlantis has been reborn. Over the hundreds and hundreds of years our order kept our secret, we longed for the opportunity to put an end to technology and the greed and power it begat._

_When our ancestors first learned that there were races of humans content with a simple life, living off the soil of their home world, they realized the ways of our people were misguided. The original Libét were denied their desire to an existence free of technology, and they vowed that regardless of the centuries that passed, their goal would be realized._

_Over the centuries, many of the Libét became scientists in order to plan the demise of the city-ship Atlantis. We thought it only fitting that we used technology to destroy technology. The method of destruction was created, honed, and implemented over many years, by many hands. Imagine our elation when all the technology available to them could not save the Alterans from beings of their own creation, and they were forced to abandon their precious city. It was the perfect situation for our plan to come to fruition. We were satisfied with the knowledge that should the city attempt to rise to prominence again it would be destroyed._

_For you to see this, you must be the current muse that does Atlantis' bidding. Whatever event has allowed Atlantis to rise from the ocean on Lantea has heralded its end. Remember this, the arrogance of the Alterans to force their lifestyle onto my ancestors has been their undoing. Had they given my ancestors the choice they desired, Atlantis would survive._

_We may never know our plan has been achieved. We go to Earth with the opportunity to live the life we choose; content in the knowledge that Atlantis either sits as an empty shell or is scattered across the ocean floor. Either way, Atlantis is no more."_

As the hologram faded, Sheppard whispered, "Looks like there was enough arrogance to go around."

Atlantis spoke, _"I do not understand."_

"Just talking to myself; we're running out of time. What do I do?"

_"Look for a conduit that leads to the small zero point module from the larger one, then trace it back to the console in the center where the control disks are located."_

Sheppard located the thin conduit attached to the main power device, then followed it up and across the ceiling and down to the smaller ZPM unit. From there, three power conduits passed to each of the three consoles along the wall.

"Okay, I've got the conduit leading to the console, now what? "

"There are six crystals to the left, these crystals should be the data, power, and control crystals for the power source; pull them."

His hands were shaking, and he was breaking out in a cold sweat, tying to ignore the pain in his head and in his chest where the shrapnel struck. Trembling, he touched a crystal with the intent of pulling it from its slot. Instead, an arc of electricity jumped from the console and struck him, throwing him to the deck.

Stunned from the surge of electricity traveling through his body, Sheppard lay sprawled across the tile, his nerve endings raw and tingling. As he tried to catch his breath, he realized time was slipping away, and he had to get up. Using the center console as a brace, he pulled himself to his feet.

"What…what the hell…w-was that?"

_"Another obstacle, they have rigged the power to flow both across and through the crystals. There is no manual way to defuse the explosion."_

"Crap…so what else can I do?"

_"You can use the gene to override the system, visualize the system powerless. That is your only choice."_

"Great…it all comes down to choices."

Sheppard gripped the center console tighter and concentrated. Focusing was difficult and his mind drifted to now much time was left, wondering if McKay and Ronon had gotten away.

_"Concentrate, you must concentrate."_

Ragged streaks of burning pain pulsated through Sheppard's head, as he fought to keep one single thought, turn the power off. Waves of nausea began to flow through him; his body bathed in sweat. The resistance against his thoughts was strong, but he forced himself to keep his attention on his task; the harder he pushed, the more the pain intensified.

Warmth spread across his upper lip, the metallic taste of blood seeping into his mouth. He swayed, gripping the console tighter wanting to give up, the crushing, blinding pain becoming too much. Then the lights flickered, and he could feel the resistance fading; one more minute, just one more minute that's all he needed.

_"Concentrate, you are almost done."_

Despite the pain, Sheppard felt tranquility flood through his body as she spoke to him; leaving him with only one thought, he had to save Atlantis. Concentrating as hard as he could, he sensed the power in the chamber fade. With one final thought before he blacked out, he whispered, "Open door."

~ooOoo~

"When the hell is he going to wake up?"

Teyla covered her face with her hands. "Rodney, as Doctor Beckett has repeatedly explained, John will wake up when he is ready."

Ronon was leaning against the wall; arms folded against his chest, his chair resting on two legs. The chair hit the floor with a resounding thud. "McKay, if you don't shut up…"

"What? I'm just asking a question."

Lip curling, Ronon stared at McKay, who withered under the Satedan's gaze. "Little man, do not ask that again."

McKay raised his right hand, finger in the air, but before he could fire back at Ronon, Weir walked in. The tension in the room was palpable, and she quickly realized that Sheppard's teammates were exhausted and getting testy.

"How about the three of you a take a break, I'll stay with the colonel."

Ronon frowned, "No need as long as McKay keeps his mouth shut."

Weir blew out a long breath, "You all need to get some rest; you're not helping John this way. Do I have to order you?

Teyla stood up, then sat back down again, her frustration evident. "It is just Doctor Beckett says there is no reason for the colonel to be unconscious, yet it has been four days since he diffused the bomb. We are worried, what if he does not regain consciousness?"

Ronon's chair once again was leaning on two legs; his arms refolded. He grunted, "He will."

Weir sat in an empty chair at the foot of Sheppard's bed, "Teyla...John went through a lot. From what Carson says, his brain was extremely stressed during this ordeal. Add that to the physical injuries he's suffered, the concussion from the fall, not to mention the impact from that large piece of debris that badly bruised his chest. Thank goodness he was wearing protection gear, otherwise…" She uttered a small sigh, "It's no wonder John needs rest."

They lapsed into silence, each lost in their own thoughts. Ten minutes passed before Carson Beckett entered Sheppard's private room, and his friends were still sitting in silence. He walked to Sheppard's bedside, took a quick look at the colonel's vital signs, and checked his pupil response. He then turned to find four faces starting at him.

"Ya look like wee puppies waiting for a treat." A slight frown crossed his face, "I could order you out of the infirmary, get Lorne to bring in the Marines to clear you out."

Ronon raised an eyebrow, "How many Marines?"

Beckett flashed a wry grin, "Probably not enough. Look, John is resting comfortably. All his brain activities are normal, including the newly activated section, he's healing from the serious bruising…"

Weir interrupted, "He was bleeding from the nose and ears when we got to him. There's no indication that he has any brain damage?"

"I canna answer that until he wakes up," Beckett saw how uncomfortable they all were and quickly added, "but there is no indication of that. You all need rest; John may need you more when he wakes up, he's been through a lot. Having an alien entity…machine or not…mess with your brain has to be a bit disconcerting. " He was met with stares. " Alright, I'm going to order food for you, since I can't get you to budge."

~ooOoo~

Atlantis waited, as his team waited.

She was aware before the others that he was awakening. Slipping into his consciousness, she was patient until he realized she was with him.

"Atlantis, that you?"

_"Yes, I am here."_

"Where's here?"

_"You are in the infirmary."_

"Oh…yeah, well…what else is new. Wait…you're here, so we did it?"

_"Yes, you managed to diffuse the device with moments to spare."_

"Moments, huh…that unusual…mostly it's seconds. I have a lot of questions."

_"My muses usually do; I will answer all of your questions in due time. Now, you need to awaken. Your friends are quite worried about you."_

"Atlantis…thanks."

_"I will be here when you are ready."_

~ooOoo~

Rodney McKay reached for the last sandwich, only to have it snatched out of his hands by Ronon.

"Give that back," Rodney's shoulders dropped, "That's the last one."

"You've had two already, besides…you eat too much." Ronon consumed the turkey sandwich in two bites.

"And you ...glutton of the month... certainly don't eat too much."

Teyla, clearly irritated, handed McKay half of the sandwich she was eating, "If it shuts both of you up, you can have mine."

"Thanks…" McKay began to nibble on the sandwich, not noticing Teyla shake her head.

"Any…thing left to…eat?"

McKay, Ronon and Teyla looked at each other, then spun their heads in unison toward the bed. Teyla was on her feet first, and rushed to Sheppard.

Her smile beaming, Teyla grabbed Sheppard's hand, "John you are awake."

"Yeah…and hungry."

Ronon chuckled, "Sorry, Sheppard; Rodney ate the last sandwich."

"I did not."

Teyla shushed the two men, "Rodney, go get Dr. Beckett."

Sheppard's mouth was dry and he threw his hand toward the nightstand, "Water."

Teyla poured a glass of water and gave him a sip, "No more until Doctor Beckett gets here." She straightened the pillow under Sheppard's head, "How are you feeling?"

"Like an elephant's sitting on my chest but otherwise okay; head's not hurting."

"We were very worried; it has been nearly five days since you lost consciousness."

"F-five? Oh…."

Beckett arrived, a grin on his face and a nurse in tow, "You're awake, Colonel; that's wonderful news." He asked Sheppard a series of cognitive questions, satisfied with the answers. He looked up at the nurse, "David... I want to do a scan on the colonel, let's get that set up, alright?" David nodded and left to get the scanner ready.

He turned his attention back to his patient, "Rodney tells me you are hungry; that's good. As soon as we get this scan done, I'll order a meal for you. You seem to have all your faculties. After what you've been through, laddie, that's a wee miracle."

David returned to announce the scanner was ready. Beckett said, "Okay, let's get you checked out."

Sheppard fell asleep shortly after the scan was completed, waking up six hours later. As promised, Beckett ordered a meal for him, and as he ate, talked with his team, Weir, and Major Lorne.

"What happened after I blacked out?"

McKay answered, "Well the door opened…"

About to take a spoonful of green jello, Sheppard interrupted, "Yeah…I remember thinking to open the door right before the power dropped."

"It was good thinking…"

Sheppard pointed the spoon at McKay, "Wait…how many minutes to spare before the blast?

McKay looked sheepish, glancing at Ronon, who answered, "Seven."

"Seven…which means you disobeyed my orders and stayed." Sheppard chewed on his bottom lip, glaring at his two friends. "I told you to leave. You could've died."

"Yeah…well, we didn't" McKay snarked, "so…the door opens, and we find you, unconscious, bleeding from your nose and ears."

Ronon interjected, "McKay panicked, thought you were dead."

"I did not panic; I was concerned."

Ronon grinned, "He panicked."

Weir raised her hand to stop the bickering, "Let me tell John what happened. Major Lorne, a Marine squad and CEs, Beckett and a medical team and I were waiting in two jumpers just outside the blast range. When Rodney radioed us, we returned to Atlantis. Beckett and the medical team got to you within ten minutes."

"Ten minutes to me," Sheppard's mouth twisted, "that means you were less than five minutes from the city. If Atlantis had blown up, that might not have been far enough."

Lorne replied, "Colonel... I took the jumpers to a high altitude. We…we…were waiting."

"What Lorne is trying to say, is that we were waiting for your jumper to arrive. Besides, we needed confirmation if Atlantis did explode." Elizabeth was solemn, "Thanks to you; Atlantis is still here, and everything is operating again."

Sheppard looked away from Weir, "No, thanks to Atlantis."

The group fell quiet as they realized how close they had come to losing the city they loved. As Doctor Beckett joined them, McKay broke the silence.

"What happened in that room, Sheppard?"

Sheppard glanced toward McKay and for the first time, realized Rodney was holding the small ZPM. "McKay, see you have a new toy."

McKay grinned, "This is really cool. Can you find out from Atlantis…"

"Enough Rodney, you can ask John about that when he's stronger." Weir shrugged, "I think he's adopted it, calls it Junior."

Sheppard laughed then grimaced, his hand going to his chest. Before he could reply to Weir, Beckett asked, "You up to talking this much?"

Sheppard nodded, "I'm fine. You need to know what the Libét did. "

For the next hour, Sheppard recounted the past few weeks as Atlantis initiated communications with him and what he had learned about her origin, and what he knew about the Libét. They were so engrossed with his story that they asked few questions, when he finished, they were silent.

Reaching for the coffee that Beckett finally allowed him to have, Sheppard surveyed his friends, then remarked, "I was so caught up in the minute-by-minute of all this, I didn't think about what was happening. Pretty crazy stuff."

Teyla spoke, her voice distant, "I cannot understand how the Libét contained their anger for so long. How they did not reveal who they were? Surrounded by all this technology, it is overwhelming; I cannot imagine being resentful of it and having to live among it."

Weir cocked her head, "You know, the Alterans from what we learned were very disciplined people. Add a vehement belief to such a rigid persona and…" She threw up her hands, "They were certainly dedicated, very cult like."

"There are six other city-ships?" McKay looked wistful.

Sheppard nodded, "That's what Ludo said."

"Can you ask Atlantis if she knows something, anything about them?"

"Sure Rodney but I don't know if she'll have any information about what happened to the others."

"But the location of this planet, Altera Seven, she probably knows where it is."

Sheppard nodded, "I'll ask her; there's a lot to ask her."

Beckett stood up, "One more question, then you sleep. Why you, why do you have such a strong gene?"

"I have no idea?"

"You aren't a direct descendent of the Ancients, laddie, and in the ten thousand years since the Ancients settled on Earth, odds are that gene would have mutated. For us to even be able to utilize the gene without it being synthetic is surprising. Yet, according to what Atlantis has told you, you have an exceptionally strong gene."

Sheppard shrugged, "I can't answer that, you guys are the scientists…you're going to have to tell me." Sheppard's voice trailed off, and his eyes closed. Beckett motioned everyone out of the infirmary. For the first time in nearly a week, his friends got a good night's sleep.

~ooOoo~

Two days of cajoling by Sheppard and Beckett finally gave in and released him from the infirmary to his quarters. He slipped out, not bothering to change out of the infirmary scrubs, when his team left for lunch; he wanted some time to decompress alone.

As the doors slid closed behind him, he sighed, leaning against the wall for a moment, thankful for the quiet. Contentment washed over him as he felt the familiar vibration of Atlantis coursing through him. Atlantis. She spoke to him briefly after he woke, saying she would wait until he was ready to communicate with her. She felt he needed time to rest.

As he headed to the bathroom, tugging off the scrubs as he went, he thought she was right; so much happened during the last few weeks, he needed some down time. He stepped into the shower, hot water cascading across his bruised and sore body. His mind drifted, all the events of the last weeks flashing through his memory. Three years ago, a shower would have been in a cramped stall in a stark and always cold bathroom on Antarctica. Now he was standing in a spacious shower on a planet in another solar system, possessing an ability he could have never conceived.

Sheppard forced his mind to clear and for the next minutes, he thought of nothing but the hot water massaging the stiffness and pain away. Eventually, deciding he couldn't stay in the shower all day, he thought the water stream off and engaged the warm air vents to dry off. Stepping out of the shower, he walked straight to the windows. From his vantage point, he could see the edge of the pier and the buildings between. Armed with the knowledge of Atlantis' past, he wondered what secrets she held from her thousands of years of existence. He expected it could take a lifetime to discover her history.

Pulling a t-shirt and track pants from a dresser drawer, Sheppard slipped them on, grabbed a bottled water from a cooler, and laid down on his bed.

"Atlantis, you there?"

_"I am."_

"We have a lot to talk about."

_"I know."_

The end…


End file.
